Related Experiment Video
Updated: Jun 10, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and
1Department of Ecology, Montana State University, Bozeman, MT, USA. skalinowski@montana.edu
Abstract:
One of the primary goals of population genetics is to succinctly describe genetic relationships among populations, and the computer program STRUCTURE is one of the most frequently used tools for doing so. The mathematical model used by STRUCTURE was designed to sort individuals into Hardy-Weinberg populations, but the program is also frequently used to group individuals from a large number of populations into a small number of clusters that are supposed to represent the main genetic divisions within species. In this study, I used computer simulations to examine how well STRUCTURE accomplishes this latter task. Simulations of populations that had a simple hierarchical history of fragmentation showed that when there were relatively long divergence times within evolutionary lineages, the clusters created by STRUCTURE were frequently not consistent with the evolutionary history of the populations. These difficulties can be attributed to forcing STRUCTURE to place individuals into too few clusters. Simulations also showed that the clusters produced by STRUCTURE can be strongly influenced by variation in sample size. In some circumstances, STRUCTURE simply put all of the individuals from the largest sample in the same cluster. A reanalysis of human population structure suggests that the problems I identified with STRUCTURE in simulations may have obscured relationships among human populations-particularly genetic similarity between Europeans and some African populations.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
What is Population Genetics?
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Mutation, Gene Flow, and Genetic Drift
Genetics of Speciation
Mechanistic Models: Compartment Models in Individual and Population Analysis

